diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.
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| Abstract | Summary: The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops. We demonstrate this functionality by detecting differences between ENCODE ChIA-PET samples and relate looping to variability in epigenetic state. Availability and implementation: Diffloop is implemented as an R/Bioconductor package available at . Contact: aryee.martin@mgh.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online. |
| Year of Publication | 2018
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| Journal | Bioinformatics
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| Volume | 34
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| Issue | 4
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| Pages | 672-674
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| Date Published | 2018 02 15
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| ISSN | 1367-4811
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| DOI | 10.1093/bioinformatics/btx623
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| PubMed ID | 29028898
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| PubMed Central ID | PMC5860605
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